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Metabolic Engineering 2017.Pdf Metabolic Engineering 42 (2017) 19–24 Contents lists available at ScienceDirect Metabolic Engineering journal homepage: www.elsevier.com/locate/meteng Enhancing erythritol productivity in Yarrowia lipolytica using metabolic MARK engineering Frédéric Carlya, Marie Vandermiesb, Samuel Telekb, Sébastien Steelsb, Stéphane Thomasc, ⁎ Jean-Marc Nicaudc, Patrick Fickersb, a Unité de Biotechnologies et Bioprocédés, Université Libre de Bruxelles, Belgium b Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux Agro-Bio Tech, Belgium c Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France ARTICLE INFO ABSTRACT Keywords: Erythritol (1,2,3,4-butanetetrol) is a four-carbon sugar alcohol with sweetening properties that is used by the Yarrowia lipolytica agrofood industry as a food additive. In this study, we demonstrated that metabolic engineering can be used to Erythritol improve the production of erythritol from glycerol in the yeast Yarrowia lipolytica. The best results were obtained Metabolic engineering using a mutant that overexpressed GUT1 and TKL1, which encode a glycerol kinase and a transketolase, Glycerol kinase respectively, and in which EYK1, which encodes erythrulose kinase, was disrupted; the latter enzyme is involved Transketolase in an early step of erythritol catabolism. In this strain, erythritol productivity was 75% higher than in the wild Erythrulose kinase type; furthermore, the culturing time needed to achieve maximum concentration was reduced by 40%. An additional advantage is that the strain was unable to consume the erythritol it had created, further increasing the process's efficiency. The erythritol productivity values we obtained here are among the highest reported thus far. 1. Introduction as mannitol, and organic acids which renders the downstream proces- sing more challenging. Recently, Yarrowia lipolytica has also been found Erythritol (1,2,3,4-butanetetrol) is a four-carbon sugar alcohol with to be an efficient erythritol producer (Rymowicz et al., 2008; Yang sweetening properties that is used by the agrofood industry as a food et al., 2014; Park et al., 2016; Mirończuk et al., 2016). additive (E968). Erythritol is noncariogenic and has been determined to Y. lipolytica is a non-conventional model yeast species that is well- be safe for human consumption even when high doses are consumed known for its unusual metabolic properties (Fickers et al., 2005; daily (Bernt et al., 1996; Kawanabe et al., 1992). It has extremely low Nicaud, 2012). Because it can secrete large amounts of proteins and digestibility and does not modify blood insulin levels (Munro et al., metabolites of biotechnological interest, Y. lipolytica has several 1998). Erythritol is widespread in nature and has been found in industrial applications, including heterologous protein synthesis and seaweed, fungi, fruit, and fermented food, although always at low citric acid production, and has been accorded GRAS status (Fickers levels (Moon et al., 2010). It is also produced by osmophilic micro- et al., 2005; Zinjarde, 2014). Y. lipolytica is highly proficient at organisms in response to osmotic stress (Hallsworth and Magan, 1997). producing erythritol and can use raw glycerol instead of glucose as its Although erythritol can be produced chemically from dialdehyde main carbon source (Rymowicz et al., 2008; Almeida et al., 2012). Raw starch, this process has never been industrialized due to its low glycerol is a byproduct of the biodiesel production or fat industries (i.e. efficiency. Instead, erythritol is most commonly generated from glucose fat saponification, stearin synthesis) and is thus available in large via fermentation processes using osmophilic yeasts (Moon et al., 2010) quantities at lower price than glucose. Moreover, glycerol allows higher namely Aurobasidium sp. (Ishizuka et al., 1989), Trigonopsis variabilis production yields as compared to glucose, making the erythritol (Kim et al., 1997), Torula sp. (Lee et al., 2000), Candida magnoliae (Ryu production process more profitable. (Rymowicz et al., 2008; et al., 2000), Pseudozyma tsubakaensis (Jeya et al., 2009), and Moniliela Tomaszewska et al., 2012; Rywińska et al., 2013). The synthesis of sp. (Lin et al., 2010). Despite the some of these processes have been erythritol from glycerol is not a redox-balanced reaction, as it requires a developed at industrial scale, they suffer from the high cost of the net amount of oxidized cofactors. However it is more advantageous fermentation media and the production of unwanted byproducts such than using glucose since synthesis of erythritol from the latter consumes ⁎ Correspondence to: Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Passage des Déportés, 2, 5030 Gembloux, Belgium. E-mail address: pfi[email protected] (P. Fickers). http://dx.doi.org/10.1016/j.ymben.2017.05.002 Received 1 March 2017; Received in revised form 2 May 2017; Accepted 19 May 2017 Available online 22 May 2017 1096-7176/ © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved. F. Carly et al. Metabolic Engineering 42 (2017) 19–24 2. Materials and methods 2.1. Strains, media, and culture conditions The Escherichia coli and Y. lipolytica strains used in this study are listed in Supplementary table 1. The E. coli strains were grown at 37 °C in Luria-Bertani medium supplemented with kanamycin sulfate (50 mg/L; Sigma-Aldrich). The Y. lipolytica strains were grown at 28 °C in YNB medium supplemented to meet the requirements of auxothrophs (Barth and Gaillardin, 1996); EG medium (glycerol 50 g/ Fig. 1. Pathway used by Y. lipolytica to synthesize erythritol from glycerol. DHAP: L, yeast extract 5 g/L and peptone 5 g/L); EPF medium (glycerol 100 g/ dihydroxyacetone phosphate; GA3P: glyceraldehyde-3-phosphate; GK: glycerol kinase; L, yeast extract 1 g/L, NH4Cl 4.5 g/L, CuSO4 0.7 mg/L, MnSO4·H2O GDH: glycerol-3P dehydrogenase; TIM: triosephosphate isomerase; TK: transketolase; ff E4PP: erythrose-4P phosphatase; ER: erythrose reductase; and EK: erythrulose kinase. 32 mg/L, and 0.72 M phosphate bu er pH 4.3) or EPB medium Dotted arrows represent the hypothetic catabolism pathway of erythrulose-P according to (glycerol 150 g/L, NH4Cl 2 g/L, KH2PO4 0.2 g/L, MgSO4·7H2O 1 g/L, Paradowska and Nitka (2009). NaCl 25 g/L and yeast extract 1 g/L). For solid media, agar (15 g/L) was added. Shake-flask cultures were performed in triplicate for eight days reduced cofactors that must be replenished through glucose oxidation. in a rotary shaker at 28 °C and 190 RPM. After 72 h of preculturing in When erythritol is synthesized from glycerol, the latter is first 35 mL of EG medium, cells were transferred to a 250 mL-flask contain- phosphorylated by a glycerol kinase (GK) before subsequently being ing 35 mL of EPF medium; initial optical density at 600 nm (OD600) was dehydrogenated by a glycerol-3P-dehydrogenase (GDH), giving rise to 0.4. Bioreactor cultures were performed in duplicate in a 2-L Biostat B- dihydroxyacetone phosphate (DHAP) (Fig. 1). DHAP is then converted Twin fermentor (Sartorius) containing 1 L of EPB medium and kept at by a triosephosphate isomerase (TIM) into glyceraldehyde-3-phosphate, 28 °C. Stirrer speed was set to 800 RPM, and the aeration rate was 1 L/ which enters into the pentose phosphate pathway, where a transketo- min. The pH was automatically maintained at 3.0 by the addition of lase (TK) converts it into erythrose-4-phosphate. The latter is depho- 20% (w/v) NaOH or 40% (w/v) H3PO4. sphorylated by an erythrose-4P phosphatase (E4PP) and reduced by an erythrose reductase (ER) to become erythritol. Depending on experi- 2.2. Quantifying biomass, glycerol concentration, and erythritol mental conditions, Y. lipolytica can also use erythritol as its main carbon concentration source. We have recently highlighted that this catabolic pathway in Y. lipolytica is similar to those present in other yeasts, including Lipomyces Biomass was determined gravimetrically after the cells had been starkeyi (Carly et al., submitted for publication)(Fig. 1). Furthermore, washed and dried at 105 °C for 24 h. Glycerol and erythritol concentra- we identified the gene EYK1 (YALI0F01606g), which encodes an tions were determined using an HPLC (Agilent 1200 series; Agilent erythrulose kinase (EK). In Y. lipolytica, disruption of EYK1 impairs Technologies) equipped with a refractive index detector and an Aminex growth on erythritol. HPX-87H ion exclusion column (300×7.8 mm; Bio-Rad). Elution was Although most of the genes involved in erythritol synthesis have performed using 15 mM trifluoroacetic acid as the mobile phase at a been described, little is known about their regulation at finer scales or flow rate of 0.5 mL/min and a temperature of 65 °C. about the pathway's limiting steps. To date, most studies seeking to improve erythritol production have used wild type strains or randomly 2.3. General molecular biology techniques generated mutants and have focused on optimizing the culture medium or culturing conditions (Rymowicz et al., 2008; Yang et al., 2014; Standard media and techniques were used for E. coli (Sambrook Mirończuk et al., 2015; Rakicka et al., 2016). However, some recent et al., 1989), and the media and techniques used for Y. lipolytica have research using Y. lipolytica has underscored the potential utility of been described elsewhere (Barth and Gaillardin, 1996). The restriction genetic engineering
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